Microbiology of Ethnic Fermented Foods and Alcoholic Beverages of the World

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Background

We presume that there may be more than 5000 varieties of common and uncommon fermented foods and alcoholic beverages being consumed in the world by billions of people. Global fermented foods are classified into 9 major groups on the basis of substrates (raw materials) used from plant/animal sources: fermented cereals, fermented vegetables and bamboo shoots, fermented legumes, fermented roots/tubers, fermented milk products, fermented and preserved meat products, fermented, dried and smoked fish products, miscellaneous fermented products, and alcoholic beverages. Fermented foods are the hubs of consortia of microorganisms, which transform the chemical constituents of raw materials of plant/animal sources during in situ/ex situ fermentation, thereby enhance the nutritional value with health-promoting bioactive compounds.

Common genera of the lactic acid bacteria isolated from various fermented foods globally are Alkalibacterium, Carnobacterium, Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Oenococcus, Pediococcus, Streptococcus, Tetragenococcus, Vagococcus and Weissella. Species of Bacillus are reported for alkaline-fermented foods of Asia and Africa. The association of several species of Kocuria, Micrococcus (members of the Actinobacteria) and Staphylococcus (belonging to the Firmicutes) have been reported for fermented milk, fermented meat and fish products. Species of Bifidobacterium, Brachybacterium, Brevibacterium, and Propionibacterium have been isolated from cheese and species of Arthrobacter and Hafnia from meat fermentation. Enterobacter cloacae, Klebsiella pneumoniae, K. pneumoniae subsp. ozaenae, Haloanaerobium, Halobacterium, Halococcus, Propionibacterium, and Pseudomonas, are also present in numerous fermented foods

Genera of yeasts reported for fermented foods, alcoholic beverages and non-food mixed amylolytic starters are Brettanomyces, Candida, Cryptococcus, Debaryomyces, Dekkera, Galactomyces, Geotrichum, Hansenula, Hanseniaspora, Hyphopichia, Issatchenkia, Kazachstania, Kluyveromyces, Metschnikowia, Pichia, Rhodotorula, Rhodosporidium, Saccharomyces, Saccharomycodes, Saccharomycopsis, Schizosaccharomyces, Sporobolomyces, Torulaspora, Torulopsis, Trichosporon, Yarrowia and Zygosaccharomyces. Major roles of filamentous fungi in fermented foods and alcoholic beverages are mainly production of enzymes and also degradation of anti-nutritive factors. Species of Actinomucor, Amylomyces, Aspergillus, Monascus, Mucor, Neurospora, Parcilomyces, Penicillium, Rhizopus and Ustilago are reported for many fermented foods, Asian non-food amylolytic starters and alcoholic beverages.

Direct DNA extraction from samples of fermented foods, commonly called culture-independent methods, is nowadays frequently used in food microbiology to profile both cultivable and uncultivable microbial populations from fermented foods. Amplified ribosomal DNA restriction analysis (ARDRA) and denaturing gradient gel electrophoresis (DGGE) techniques developed to profile microbial communities directly from fermented foods, and are based on sequence-specific distinctions of 16S rDNA or 26S rDNA amplicons produced by PCR.

Application of next generation sequencing (NGS) such as metagenomic approaches by using parallel pyrosequencing of tagged 16S rRNA gene amplicons provide information on microbial communities as profiled in kimchi, a naturally fermented vegetable product of Korea, nukadoko, a fermented rice bran of Japan, narezushi, a fermented salted fish and cooked rice of Japan, and ben-saalga, a traditional gruel of pearl millet of Burkina Faso. A proteomics identification method based on protein profiling using matrix-assisted laser desorption ionizing-time of flight mass spectrometry (MALDI-TOF MS) is used to identify bacteria in fermented foods. NGS has revealed the new dimension of microbial ecology comprising both cultivable and uncultivable microorganisms in many ethnic fermented foods and beverages of the world.

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